I just started using MFR recently, and was amazed as how well everything worked. I'm in 1.5.2 now, and will be using it more often since I don't have RP to rely on. I love the mob spawner. It's a great way to farm the annoying drops... Ender eyes, ghast tears, etc. Find a mob, capture it in a safari net, and replicate.
I've worked with the grinders. They work well enough, but they won't kill iron golems. That might make it a little OP and too easy to get iron. The mob spawner will duplicate them though.
I will be setting up some mini farms to grow different materials for the bio-reactor and for turning into methane with GT. Still have a way to go with it though. Most of the issues I have with MFR has little to do with the machines, and more with building the building and infrastructure required to connect all the machines together to make it work. Since each machine has a single purpose and the output of one feeds others, the piping can get quite messy when trying to connect it all together. That is the real challenge with using this mod.